From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Nov 25 2009 - 03:42:35 CST
I have search the mailing list for related problems, but none of the threads
seem to offer a conclusive solution.
NAMD exits with the following message:
FATAL ERROR: Multiplicity of Paramters for diehedral bond C NH1 CT1 C of 1
This is probably related to the topology file for the MTSL spin label
(residue CMTS in the psf file), but for the life of me, I cannot figure out,
where the dihedral is duplicated.
> The psf file was generated with CHARMM and written using "write psf card
xplor" at BOMLEV -1.
What would be the best way to find the duplicated dihedral angle? Could I
perhaps just make NAMD ignore the multiplicity (like CHARMM obviously does)?
PS: should I be concerned about the following NAMD warnings?
Warning: Ignored 5860 bonds with zero force constants.
> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
I have attached the following files:
(My e-mail message has not shown up in the mailing list, perhaps because of
an attachment, that is why the following files have been uploaded to
ekvinatoksin.log -- the log file form NAMD
> ekvinatoksin.start.1ns.conf -- the NAMD configuration file
> par_all27_prot_lipid_pf.inp -- CHARMM27 parameter file
> top_all27_prot_lipid_pf.inp -- CHARMM27 topology file
> top_cmtssl2_c22_pf.inp -- topology file of the spin label
> write_namd_psf.inp -- Charmm inputfile used to generate the PSF
> write_namd_psf.inp -- Charmm output file of the PSF generation
> weqii-i18c.namd.psf -- the resulting problematic PSF file
Thank you for your help & best regards,
> Ajasja Ljubetic
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